Date

5.07 Biological Chemistry Syllabus - Fall 2015 Instructors: Professors Alexander M. Klibanov (AMK) and Alice Y. Ting (AYT)

DateLect. No.Lecture TopicReading (Voet et al., 3rd edn.)(Voet et al., 4th edn.)Lecturer

Wed., Sept. 91Organization of 5.07.Life, cell, metabolic pathways, regulation, building blocksChapter 1Chapter 1AMK

Fri., Sept. 112Water, hydrogen bonds, amino acids Chapters 2 and 4Chapters 2 and 4AMK

Mon., Sept. 143Primary and secondary structures of proteins (PSet 1 due) Chapters 5 (91-114) and 6 (125-134)Chapters 5 (93-116) and 6 (125-136)AMK

Wed., Sept. 164Tertiary and quaternary structures of proteinsChapters 6 (134-151) and 7 (176-197)Chapters 6 (136-152) and 7 (176-196)AMK

Fri., Sept. 185Enzymes and mechanisms of catalysis Chapter 11 (322-339 and 347-359)Chapter 11 (315-331 and 339-350)AMK

Mon., Sept. 216Enzyme kinetics(PSet 2 due)Chapter 12 (363-376)Chapter 12 (355-368)AMK

Wed., Sept. 237Enzyme inhibition and controlChapter 12 (377-393)Chapter 12 (368-385)AMK

Fri., Sept. 258Introduction to metabolismChapter 14 (448-459, 475-482)Chapter 14 (436-446 and 462-468)AMK

Mon., Sept. 289Phosphoryl group transfer; ATP(PSet 3 due)Chapter 14 (459-469)Chapter 14 (446-456)AMK

Wed., Sept. 3010Redox cofactorsChapters 11 (326-328) and 14 (469-474)Chapters 11 (319-320) and 14 (456-461)AMK

Fri., Oct. 211Chemistry of sugarsChapter 8 (219-234)Chapter 8 (217-230)AMK

Mon., Oct. 5Exam # 1Lectures 1-8, PSets 1-3

Wed., Oct. 712Glycolysis I

Chapter 15 (485-510)Chapter 15 (472-496)AMK

Fri., Oct. 913Glycolysis II(PSet 4 due) Chapters 15 (510-520) and 16 (530-539)Chapters 15 ( 496-506) and 16 (517-525)AMK

Mon., Oct. 12NO CLASS (Columbus Day Holiday)

Tue., Oct. 1314Pyruvate dehydrogenase complex Chapter 17 (570-576)Chapter 17 (555-561)AMK

Wed., Oct. 1415TCA cycle IChapter 17 (566-570 and 576-583)Chapter 17 (551-555 and 561-568)AMK

Fri., Oct. 1616TCA cycle II(PSet 5 due)Chapter 17 (583-594)Chapter 17 (568-578)AMK

Mon., Oct. 1917Lipid structure, digestion, and transportChapters 9 (245-252) and 20 (677-687) Chapters 9 (241-248) and 20 (657-666) AMK

Wed., Oct. 2118Fatty acid oxidation Chapter 20 (688-700) Chapter 20 (667-680) AMK

Fri., Oct. 2319Electron transport chain I (PSet 6 due)Chapter 18, Chapter 18AYT

Mon., Oct. 26Exam # 2Lectures 9-18, PSets 4-6AMK

Wed., Oct. 2820Electron transport chain IChapter 18, Chapter 18AYT

Fri., Oct. 3021Electron transport chain IChapter 18, Chapter 18AYT

Mon., Nov. 222Electron transport chain II Chapter 18, Chapter 18AYT

Wed., Nov. 423Electron transport chain II Chapter 18, Chapter 18AYT

Fri., Nov. 624ATP synthase Chapter 18, Chapter 18AYT

Mon., Nov. 925DNA structure (PSet 7 due)Chapters 3 (39-50) and 24 (848-855)Chapters 3 (40-51) and 24 (821-828)AYT

Wed., Nov. 11NO CLASS (Veterans Day Holiday)

Fri., Nov. 1326Overview of DNA replication Chapter 25 (893-914) Chapter 25 (867-889)AYT

Mon., Nov. 1627DNA replication speed, sliding clamps, and clamp loaders I Chapter 25 (893-914) Chapter 25 (867-889)AYT

Wed., Nov. 1828DNA replication speed, sliding clamps, and clamp loaders II Chapter 25 (893-914) Chapter 25 (867-889)AYT

Fri., Nov. 20 29DNA replication fidelity I Chapter 25 (893-914) Chapter 25 (867-889)AYT

Mon., Nov. 23

EXAM # 3Lectures 19-27, Pset 7AYT

Wed., Nov. 2530DNA replication fidelity II Chapter 25 (893-914) Chapter 25 (867-889)AYT

Fri., Nov. 27NO CLASS (Thanksgiving Holiday)

Mon., Nov. 3031DNA replication coordination Chapter 25 (893-914) Chapter 25 (867-889)AYT

Wed., Dec. 232Modern DNA sequencing methods Chapter 3 (53-57)Chapter 3 (55-58)AYT

Fri., Dec. 433Overview of RNA transcription Chapter 26 (942-950)Chapter 26 (919-927)AYT

Mon., Dec. 734RNA transcription initiation Chapter 26 (942-950)Chapter 26 (919-927)AYT

Wed., Dec. 935RNA transcription elongation(PSet 8 due)Chapter 26 (942-950)Chapter 26 (919-927)AYT

Dec. ?FINAL EXAMLectures 1-36AMK and AYT

Instructors: Professors Alexander M. Klibanov (klibanov@mit.edu) Professor Alice Y. Ting (ating@mit.edu) Teaching Assistants: Lisa S. Cunden (lcunden@mit.edu) Nicholas A. DeLateur (delateur@mit.edu) Textbook: Voet, Voet & Pratt, Fundamentals of Biochemistry, 3rd (or 4th) edition.

Lectures: Mondays (M), Wednesdays (W), and Fridays (F), at 9-10am, all in Room 4-370. Recitations will begin the 2nd week of the semester, i.e., on Monday September 14. The recitation (R) schedule is as follows:R#1 MW 1 (36-372) Lisa Cunden R#3 TR 10 (36-144) Nicholas DeLateur R#2 MW 2 (36-372) Lisa Cunden R#4 TR 11 (36-144) Nicholas DeLateur Mid-term exams: There will be three exams during the term. They are closed book, closed notes; any necessary information will be included at the end of the exam. The dates are in the Syllabus above: Monday, October 5; Monday, October 26; and Monday, November 23. Please look at the dates and determine whether you have conflicts. (You must request the conflict exam in advance, and it will be administrated the afternoon before or morning after the scheduled exam.) If so, please contact us immediately and we will make alternative arrangements. Each exam will be worth 100 points. Final Exam: There will be a three-hour final exam held during the Final Exam period. The exam will cover the material for the entire semester and it is also closed book, closed notes. In this course everything builds on the information from the preceding lectures, so the final is cumulative. The final exam will be worth 300 points.Make-up exams: There will be none. If you miss an exam because of illness or an unexpected and urgent personal matter, please present us with a note from MIT Medical or the appropriate Dean. Under such circumstances, the points from the missed exam will not beconsidered in the calculation of your final grade (e.g., 500 total points, rather than 600 total points, if one mid-term is missed). If you miss an exam without a note from MIT Medical or a Deans authorization, you will receive a score of 0 points and this score will be factored into your final grade. Problem Sets (PSets): Every week you will be given a PSet. They are worth 10 points each. The main goal of the PSets is to focus you on important concepts covered in the lectures and the textbook. A second goal is to help you keep up with the material covered in the lectures. It is OK, and indeed encouraged, to collaborate on the PSets, but you must not copy another students work. In other words, it is important that you master the material on your own because exams are taken individually. PSets are due as indicated in the Syllabus above and should be turned in right before the lecture (9am) the day they are due in 4-370. Answers to the problem sets will be posted on the web site within 12 hours after the due date. Letter grades for the course: After the final exam, the 5.07 teaching staff will tally up the exam and problem set scores and determine what sum constitutes "Excellent, Good, Satisfactory, or Unsatisfactory" mastery of the course material. No letter grades, only numerical scores, will be assigned to the midterm or final exams. Rather, only the overall letter grades will be assigned based on the cumulative score from the entire semester.Relationship between 5.07 and 7.05: These courses offer two perspectives on the same discipline: 5.07 is only offered in the Fall, while 7.05 only in the Spring. You may take only one of these courses for credit.Website: All relevant course information (syllabus, announcements, lecture notes, lecture powerpoint presentations, PSets and answer keys, etc.) will be available on the 5.07 Stellar website: http://stellar.mit.edu/S/course/5/fa15/5.07/

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